GoConqr has a new look! Let us know what you think.

Sign up free

Flashcards

Nucleic acids

Julia Spychalska CH112: Bio-organic chemistry English 67 cards

Cards in this deck (67)

  1. 1Why are pyridine and imidazole bases?Because the lone pair of electrons on the nitrogen can accept a proton and nitrogen becomes protonated.
  2. 2Why is pyrrole not a base?The nitrogen does not have a lone pair available. In heterocyclic systems like pyrrole, the lone pair on the nitrogen of the ring is part of the conjugated aromatic system.
  3. 3What is tautomerisation?The transfer of a hydrogen from the hydroxyl or amino group to the nitrogen in the ring, with the concomitant rearrangement of some of the double bonds.
  4. 4Which tautomer of 2-hydroxypyridines is the major form?the lactam tautomer
  5. 5Which tautomer of 2-amino pyridine is the major form?the amino tautomer
  6. 6What happens if keto or amino functionalities of the base pairs are tautomerised?It causes a change in the hydrogen bonding pattern of the groups, with donors becoming acceptors and acceptors becoming donors. This can lead to base pairing to the wrong base.
  7. 7Why is RNA much less stable to hydrolysis of the phosphate ester than DNA?Due to the 2'-hydroxyl that is present in RNA, which gets involved in the chemistry and acts as an internal nucleophile, making the reaction more facile.
  8. 8What gives rise to abasic DNA?Protonation of N-7 results in loss of the base. (during cleavage of sugar-base linkage under acidic conditions)
  9. 9What is the most prevalent form of secondary structure?B-DNA
  10. 10What was the first synthetic DNA to be crystallised?A-DNA
  11. 11Why can RNA not adopt the B-DNA form?because the 2'-hydroxy group o the ribose sugar backbone prevents its formation by resulting in steric hindrance.
  12. 12Under what conditions is Z-DNA mainly found?high salt, especially high Mg2+ concentrations.
    Structure- left-handed antiparallel helix.
  13. 13Why is the uv absorbance of DNA 259nm, less than expected?Because the adjacent closely stacked base pairs interact with each other and suppress the absorbance (called hypochromicity. When the DNA is "melted", ie. separation of the two DNA strands, the uv absorbance increases. (curve graph)
  14. 14What does the unwound section of circular DNA do?it introduces a strain into the circular DNA that can result in the adoption of superhelical twists termed topoisomers.
  15. 15What is supercoiling of linear DNA driven by?The interaction between negatively charged DNA molecules (sugar phosphate backbone) and a group of positively charged proteins called histones. The complex formed is called chromatin.
  16. 16What is self-splicing?The removal of a central segment (intron) from the RNA strand and the joining together of the resultant end portions (exons) without the use of an external catalyst.
  17. 17What is Ribonuclease P?True ribozyme catalysis is shown by the protein assisted ribonuclease P which removes the leader sequence in precursor tRNA to give mature tRNA.
  18. 18What do spliceosomes do?Splicing of newly synthesised mRNA to yield mature mRNA. They are large molecules comprised of small nuclear ribonucleoprotein particles and splicing factors (proteins).
  19. 19What does peptidyl transferase do?catalyses protein synthesis to form a peptide bond.
  20. 20What enzymes cleave DNA at specific base sequences and what fragments are produced?restriction endonucleases and restriction fragments.
  21. 21Which two methods are used in sequencing the restriction fragments?The Maxam-Gilbert and Sanger (human genome) method.
  22. 22The Sanger dideoxy method uses the following:1. the purified restriction fragment to be sequenced.
    2. A primer whose sequence is complementary to the 3' -end of the fragment.
    3. the four 2'-deoxyribonucleotide triphosphates
    4. small amounts of four 2',3'-dideoxyribonucleotide triphosphates each labelled with a different dye.
  23. 23What can cause cytosine to be converted into uracil?uv light
  24. 24HOW does cytosine get replaced by uracil?Uv light causes excitation of the aromatic ring, which then reacts with water and loses its aromaticity. The amine is then replaced by an OH group and elimination of water gives uracil.
  25. 25What is dimethylsulfate?it is a mutagenic chemical and acts as a source of the potent electrophil CH3.
    This reacts with any nucleophiles on DNA, especially N-7 of guanines. Nucleophilic groups involved in H bonding are fairly resistant to attack. (e.g. NH2)
  26. 26What is vinyl chloride?a monomer of PVC
  27. 27Why does vinyl chloride cause cancer?It is not carcinogenic itself, but the body tries to excrete it but oxidising it to make it more polar for the kidney to excrete. Oxidation gives an epoxide that rearranges to give 2-chloroethanal, which then reacts with deoxyadenosine and is a potent carcinogen.
  28. 28Why are N-nitroso ureas selective anticancer agents?They are unreactive until activated biologically. Cancer cells have a higher conc of metabolic enzymes, and tumours become anoxic due to low oxygen levels and poor blood supply. Anoxia results in acidic cytoplasm (5.5), activating anticancer agent. Normal cells are not acidic enough to be damaged.
  29. 29How does Acyclovir work?The drug is activated in vivo by converting the hydroxy group into a triphosphate. Due to close resemblance to deoxyguanosine triphosphate, acyclovir triphosphate is taken by DNA polymerase to form an enzyme-substrate complex, which has no 3'-OH for replication to continue, so viral replication is destroyed.
  30. 30What is a nucleotide composed of?A nucleoside bonded to a phosphate group.
  31. 31What is a nucleoside composed of?An aldopentose sugar linked to a purine or pyrimidine base.
  32. 32What is the difference between the sugars of DNA and RNA?In DNA the sugar lacks the hydroxyl group at carbon number 2.
  33. 33What are the characteristics of pyrimidine bases and name the basesTwo nitrogens and an oxygen between the nitrogens.
    Cytosine and thymine.
  34. 34What are the characteristics of the purine bases and name the basesBicyclic system with a 5-membered ring fused with a 6-membered ring. Two nitrogens in each of the rings.
    Adenine and guanine.
  35. 35Describe Uracil structureSame structure as thymine, but is missing the 5-methyl group
  36. 36What is the difference between a nucleotide and a nucleoside?A nucleoside has no phosphate connected to the sugar.
  37. 37What bond connects nucleotides?3'-5'-phosphodiester linkage
  38. 38What is the imine group?C=N-H
  39. 39Which two pyridines hydrogen bond to themselves in pairs?hydroxypyridines and aminopyridines
  40. 40What determines which of the bases pairs with which?The hydrogen bonding pattern of the bases
  41. 41What are the products of phosphate ester hydrolysis?The phosphate group and the two alcohols.
  42. 42Why are nucleosides not stable in dilute acid?The glycosidic link rapidly hydrolyses to give a deoxypentose and nucleotide base.
  43. 43What does antiparallel mean?One strand will run from the 5'-hydroxyl to the 3-'-hydroxyl and the other strand will run opposite.
  44. 44What does right-handed mean?The strands twist in a clockwise direction.
  45. 45DNA B-form: What is the diameter of the helix and how many base pairs per turn?Diameter: 2nm
    10 base pairs per complete turn of the helix.
    Flexible structure with local variability.
  46. 46DNA- A-form: What is the diameter of the helix and how many bases per turn?Diameter:2.4nm
    11 bases per turn.
    Stiff structure and little sequence variation.
  47. 47B-DNA: what are the local differences in structure that correspond to differences in the sequence of the base pairs?Spacing of the base pairs, depth and width of the major and minor grooves.
  48. 48Why is more energy needed to disrupt the base pairing of GC rich DNA?GC base pairs form 3 hydrogen bonds which AT base pairs form 2.
  49. 49What is melting temperature?The midpoint of the melting curve.
  50. 50DNA:What happens at lower temperatures?Local breathing of DNA: a few base pairs can separate and then hydrogen bond back together again.
  51. 51What is the primary sequence of DNA?The linear sequence of the bases
  52. 52What is the secondary structure of DNA?Double helix formation
  53. 53What is circular DNA?Double stranded DNA in which the two end of each strand are joined by phosphodiester bonds. One strand can be opened and partially unwound, and then re-joined.
  54. 54What do topoisomerase enzymes do?They change the supercoiled tertiary structures by cutting, relaxing and resealing the chain.
  55. 55Why is the single-stranded nature of RNA an advantage?It allows RNA to fold back on itself via intrastrand base pairing to create folds bends, U-turns, loops, bulges and junctions.
  56. 56What are the conditions required for RNA to catalyse a reaction?high magnesium concentrations.
  57. 57Why does the ribozyme biological efficiency does not challenge that reached by proteins?Many ribozymes only act one (self-splicing) and are not recovered unchanged. Nucleic acids lack the range of hydrophobic and electrostatic interactions achieved by proteins and rely mostly on hydrogen bonding interactions.
  58. 58What is then added to the Sanger dideoxy mixture?DNA polymerase is added and a strand of DNA complementary to the restriction fragment begins to grown from the 3-end of primer. Usually, only normal deoxyribonuceltoides are incorporated into the growing chain. Occasionally a dideoxyribonuceotide is incorporated and DNA synthesis stops because there is no 3'-hydroxy to attach next nucleotide.
  59. 59How are hydroxyl radicals made?The interaction of UV light with water
  60. 60How are peroxyl radicals made?Interaction of UV light with oxygen
  61. 61How do radicals cause scission of the chain?by reacting with the sugar ring of the sugar-phosphate backbone
  62. 62How are dimers (of two pyrimidine bases) formed?The interaction of UV light with DNA
  63. 63Why are sulphur mustards good anticancer agents?The length of the molecule results in reaction of one end with one strand of DNA and reaction of the other end with the other strand of DNA, causing cross-linking of the two strands and inhibiting cell division.
  64. 64What is sulphur replaced with in sulphur mustard anticancer agents?less reactive amides.
  65. 65What are the activation steps of N-nitroso ureas?1. Urea group in the molecule is cleaved by metabolic enzymes, to give an N-nitrosoamine
    2. Under acidic conditions the N-nitrosoamine reacts to give a diazonium salt, which is very electrophilic.
  66. 66How does nitrous acid cause mutation?It reacts with the amino group of cytosine, converting cytosine to uracil.
  67. 67How does Azidothymidine (AZT) treat HIV?AZT is converted by cellular enzymes into the 5'-triphophate, which is recognised as deoxythimidine 5'-triphosphate by reverse transcriptase and is added to the growing DNA chain. This causes chain elongation to terminate because there is no 3'-OH group on which to add the next nucleotide. It is effective because it binds more strongly to viral reverse transcriptase than it does to human DNA polymerase.

Information

Description
CH112: Bio-organic chemistry (Nucleic Acids) Flashcards on Nucleic acids, created by Julia Spychalska on 26/03/2017.
Views
1
Rating

Feedback

What is it about?

What do you think of the new look?

How do you like it?